[gmx-users] nucleic acis simulation

[Maik Goette]

Take the Amber-Port:

http://folding.stanford.edu/ffamber/
http://www.gromacs.org/topologies/uploaded_force_fields/ffamber_v1.0-doc.tar.gz

But beware of renaming atoms and residues before use. If you don't 
pdb2gmx will inform you about problems.

Regards

Maik Goette, Dipl. Biol.
Max Planck Institute for Biophysical Chemistry
Theoretical & computational biophysics department
Am Fassberg 11
37077 Goettingen
Germany
Tel.  : ++49 551 201 2310
Fax   : ++49 551 201 2302
Email : mgoette[at]mpi-bpc.mpg.de
         mgoette2[at]gwdg.de
WWW   : http://www.mpibpc.gwdg.de/groups/grubmueller/


Miguel Ortiz Lombardia wrote:
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> Dear all,
> 
> This is a question from someone just taking some timid steps in this
> field. I'd like to know what force field, among those available in
> Gromacs (v. 3.3) would you consider "better" for models containing
> nucleic acids. As I understand this may be kind of a matter of taste and
> could open a somehow sterile discussion, I would suggest you send your
> opinion/arguments to my address. I would then compile a summary of the
> answers and post it later.
> 
> Thanking you in advance for your kindness.
> Cheers,
> 
> 
> Miguel
> - --
> Miguel Ortiz Lombardía
> Centro de Investigaciones Oncológicas
> C/ Melchor Fernández Almagro, 3
> 28029 Madrid, Spain
> Tel. +34 912 246 900
> Fax. +34 912 246 976
> email: molatwork at yahoo.es
> www: http://www.ysbl.york.ac.uk/~mol/
> ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
> Je suis de la mauvaise herbe,
> Braves gens, braves gens,
> Je pousse en liberté
> Dans les jardins mal fréquentés!
>                                                        Georges Brassens
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